Project Summary Craniofacial anomalies such as clefts of the lip and palate are common birth defects of complex etiology and comprise a large fraction of morbid human birth defects. They require surgical, nutritional, dental, speech, medical and behavioral interventions and impose a substantial economic and societal burden. Family and population studies have confirmed a genetic component underlying the most common form of clefting- isolated (or non-syndromic) clefting. However, despite decades of research, the precise genes involved in human clefting remain largely unknown or unconfirmed, making the understanding of the genetic basis of the disease virtually impossible. Recently, it has become practical to identify genes contributing to complex traits such as clefts by using a combination of extensive family collections, careful phenotyping, high-throughput genotyping, robust analytic strategies, fine structure mapping, mutation characterization and animal model verification. We will take advantage of our extensive experience in these areas to explore an innovative approach to gene finding by searching for genomic deletions or amplifications (called Copy Number Variants, or CNVs) that cause clefting using microarray-based Comparative Genomic Hybridization (aCGH). Deletions/amplifications of less than 1 Kb (which we call microCNVs) have been identified as causal events in Mendelian disorders; similarly, CNVs (which may vary in size between 1 Kb and many Megabases) also cause human disease (indeed, they are now considered to be common causes of disease). However, such genomic rearrangements have not yet been examined for a large cohort of cleft lip and palate patients. In this project, we will identify clefting-associated CNVs (as well as microCNVs) for both candidate gene and novel loci followed by developmental and functional validation studies of the genes within the CNVs (in the zebrafish model system) to identify the clefting-specific genes. Additionally, we will use an unprecedented microarray reuse protocol which allows 5 uses of an array without compromising the quality of the data. Together, these methods will enable large numbers of clefting samples to be analyzed rapidly at high resolution while minimizing cost. This study will provide a substantial opportunity to demonstrate how a complex genetic defect can have its component causes identified and understood as well as provide the basis for the development of cleft lip and palate diagnostic tools.